Trouble getting windowmanager properties to save it's contents with blend file
Custom properties to the bpy.types.WindowManager type don't serialize to .blend
(as if options={'SKIP_SAVE'} was set).

Your options are to use


bpy.types.Scene, but you will need to chose one scene instance to store the actual properties, and if that scene is deleted, they will be gone
Serialization: serialize your data to a string and make it the text body of a new text datablock. Give the datablock a name that starts with a dot, e.g. .my-data, to hide it in the interface. It is less likely to be removed like a scene this way.
AddonPreferences or saving to a custom configuration file - if the data is relevant to not just the current .blend, but the local Blender installation